It is believed that the systemic subtype and the positive rheumatoid factor, polyarticular subtype of juvenile idiopathic arthritis (JIA) show the least favorable outcomes for therapy; patients with systemic JIA are often resistant to recommended therapeutic modalities. We report the sequential changes to clinical and laboratory findings from pulse therapy with monthly intravenous cyclophosphamide (0.5 g/m2 body surface area) administration combined with methylprednisolone (30 mg/kg; 1 gm maximum) for 6 months, following which the medication interval was elongated to 3 months for a total of from 7 to 12 courses. Among 4 children suffering from refractory systemic JIA, 3 demonstrated clinical improvement, 2 of whom achieved clinical remission. Furthermore, we also adminstered this therapy to a girl suffering from refractory polyarticular JIA, following which she revealed clinical remission subsequent to 9 courses of such therapy. From our experience, we suggest that patients afflicted with JIA that is unresponsive to traditional medication may experience benefit from this type of pulse therapy.